From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Thu, 10 Sep 2020 11:28:47 +0000 (+0100)
Subject: JAL-2422 comments updated re ALTLOC handling
X-Git-Tag: Release_2_11_2_0~37^2~7
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=15684417a64007046f10d193d5c9363be8f88ea7;p=jalview.git

JAL-2422 comments updated re ALTLOC handling
---

diff --git a/src/jalview/ext/rbvi/chimera/ChimeraXCommands.java b/src/jalview/ext/rbvi/chimera/ChimeraXCommands.java
index b7d9ce3..d0c5671 100644
--- a/src/jalview/ext/rbvi/chimera/ChimeraXCommands.java
+++ b/src/jalview/ext/rbvi/chimera/ChimeraXCommands.java
@@ -20,15 +20,15 @@
  */
 package jalview.ext.rbvi.chimera;
 
+import java.awt.Color;
+import java.util.Arrays;
+import java.util.List;
+
 import jalview.structure.AtomSpecModel;
 import jalview.structure.StructureCommand;
 import jalview.structure.StructureCommandI;
 import jalview.util.ColorUtils;
 
-import java.awt.Color;
-import java.util.Arrays;
-import java.util.List;
-
 /**
  * Routines for generating ChimeraX commands for Jalview/ChimeraX binding
  */
@@ -132,6 +132,10 @@ public class ChimeraXCommands extends ChimeraCommands
    * Returns the range(s) formatted as a ChimeraX atomspec, for example
    * <p>
    * #1/A:2-20,30-40/B:10-20|#2/A:12-30
+   * <p>
+   * Note there is no need to explicitly exclude ALTLOC atoms when
+   * {@code alphaOnly == true}, as this is the default behaviour of ChimeraX (a
+   * change from Chimera)
    * 
    * @return
    */
@@ -153,7 +157,6 @@ public class ChimeraXCommands extends ChimeraCommands
         // TODO @P if RNA - add nucleotide flag to AtomSpecModel?
         sb.append("@CA");
       }
-      // todo: is there ChimeraX syntax to exclude altlocs?
     }
     return sb.toString();
   }